Dynamic modelling of cell cycle arrest through integrated single-cell and mathematical modelling approaches

Highly multiplexed imaging assays allow simultaneous quantification of multiple protein and phosphorylation markers, providing a static snapshots of cell types and states. Pseudo-time techniques can transform these static snapshots of unsynchronized cells into dynamic trajectories, enabling the study of dynamic processes such as development trajectories and the cell cycle. Such ordering also enables training of mathematical models on these data, but technical challenges have hitherto made it difficult to integrate multiple experimental conditions, limiting the predictive power and insights these models can generate. In this work, we propose data processing and model training approaches for integrating multiplexed, multi-condition immunofluorescence data with mathematical modelling. We devise training strategies for mathematical models that are applicable to datasets where cells exhibit oscillatory as well as arrested dynamics and use them to train a cell cycle model on a dataset of MCF-10A mammary epithelial exposed to cell-cycle arresting small molecules. We validate the model by investigating predicted growth factor sensitivities and responses to inhibitors of cells at different initial conditions. We anticipate that our framework will generalise to other highly multiplexed measurement techniques such as mass-cytometry, rendering larger bodies of data accessible to dynamic modelling and paving the way to deeper biological insights.Author summary: Advanced imaging techniques allow us to see detailed pictures of different proteins and cell changes. By using computational algorithms, we turn these static pictures into dynamic sequences to understand processes like the cell cycle better. However, combining data from different experiments is difficult and limits how well our models can predict outcomes. This study introduces new ways to process data and train models to handle complex data from various conditions. The approach is tested by using data from untreated and treated cells to create a model of the cell cycle. This model was then checked for accuracy by seeing how well it could predict how cells respond to growth factors and drugs from different starting points. In the future, this method could be used with other data types, allowing for more detailed and accurate models of cellular behavior.